That's because Vista's defragger (and 7's too IIRC) by default does not report fragments larger than 64 MB, while other defraggers do; hence the difference.
I never did like the Windows defragger (any version lol)..unbearably slow and crippled in features. Same with the freeware defraggers, many of which don't play well with the shadow copy system in Vista and 7 and also cannot defrag system files. It's not free, but my favorite defragger is Diskeeper. I am running v.2010 Pro right now on my gaming rig and it has a brilliant new feature that prevents fragmentation before it occurs, so it reduces the need for future defragging. Also, it's fully automatic so once installed it prevents fragmentation as well as defrags when necessary automatically in the background without my having to lift a finger